TB-Profiler result

Run: ERR4819082

Summary

Run ID: ERR4819082

Sample name:

Date: 20-10-2023 08:51:21

Number of reads: 3085739

Percentage reads mapped: 93.17

Strain: lineage1.1.2

Drug-resistance: Other


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin R rrs n.888G>A (0.56)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.56 streptomycin
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9047 c.1746C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9443 c.2142G>A synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576000 p.Asp218Ala missense_variant 1.0
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
mmpL5 776546 p.Met645Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.33
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.26
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.3
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.52
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.56
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.62
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.6
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.67
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.71
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.55
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.65
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.71
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.7
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.63
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.47
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.53
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.55
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.55
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.55
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.13
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.51
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.41
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.31
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.24
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.26
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.27
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.3
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.27
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.22
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.22
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.21
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.27
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.23
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.25
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.31
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.43
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.23
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.26
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.28
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.27
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.23
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065305 p.Ala296Val missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 0.99
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0